Software: Nanolyse
Description
Nanolyse is a tool to remove reads mapping to the lambda phage genome from a fastq file.
Available Versions
| Unspecified: | 1.2.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/nanolyse and its home page on Github.
Commands
- NanoLyse
Module
You can load the modules by:
module load biocontainers
module load nanolyse
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
To run Nanolyse on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=nanolyse
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers nanolyse
gunzip -c reads.fastq.gz | NanoLyse | gzip > reads_without_lambda.fastq.gz